Naked Scientists - 05.11.20 - Genetics, DNA Extraction and the Human Genome Project
This week we unravel the secrets of DNA as Darren Grafham discusses the importance of sequencing genomes and how the Human Genome Project has improved medicine, Mike Majerus reveals why we look different from worms despite sharing genetic information, Anna Lacey interviews BBC producer Mike Salisbury about the new David Attenborough series, Life in the Undergrowth, and Kitchen Science goes back to school for a live DNA extraction experiment.
In this episode
Opening Up To Mouth Cancer
DNA is found within all our cells, and contains the genetic instructions that tell our cells when to grow and multiply, and when to stop. Cancer starts when DNA gets damaged so the cell cannot understand these instructions and starts to multiply out of control, to make a tumour. Mouth cancer is on the increase in the UK - rates have gone up by a quarter in the past decade, and in men in their forties and fifties, we've seen the number of cases of mouth cancer double. But many people don't even know the disease exists. Cancer Research UK did a survey and found that one in five people have never heard of mouth cancer, so the charity has launched an awareness campaign this week to highlight the disease. They also found that while three-quarters of people surveyed knew that smoking could increase your risk of mouth cancer, only a quarter knew that drinking alcohol also increased the risk. Cancer Research UK experts think that around three out of every four cases of the disease are caused by smoking and drinking. And it's not just binge drinkers, it's the total amount of alcohol you drink throughout the week that increases your risk of mouth cancer - so we could all benefit from cutting down on the booze and quitting smoking. But what should you look for? The early symptoms of mouth cancer include sores, mouth ulcers, a hoarse voice or sore throat, red or white patches or lumps that don't go away after three weeks. So if you spot anything funny that is there for three or four weeks, then get along to your GP or dentist and get yourself checked out. You can find out more about Cancer Research UK's mouth cancer campaign at www.openuptomouthcancer.org.uk.
Japan Airlines Aims To Cut Soaring Carbon Dioxide Levels
A joint initiative between the Japanese government and Japan Airlines recently got off to a flying start with the launch of the first commercial aeroplane equipped to provide real-time measurements of atmospheric carbon dioxide and other greenhouse gases along its flight path. The project, which will eventually see five planes monitoring the atmosphere along their routes between Tokyo and Australia, Asia and Europe, aims to provide valuable environmental data, at low cost, to help scientists build up a clearer picture of carbon dioxide emissions over Asia. The planes collect air samples from the front of the plane (to avoid sucking in their own exhaust) and use light to determine the composition of the gases they collect. Signficantly, this project, which builds on an earlier initiative, will provide the first clear picture, in three dimensions, of atmospheric carbon dioxide concentrations over a large area. Until now such measurements were not feasible, nor viable, to make on earth or from space.
- Life in The Undergrowth
Life in The Undergrowth
with Anna Lacey interviews the series producer Mike Salisbury, from the BBC Natural History Unit in Bristol
Mike - It's called Life in the Undergrowth, and it's about everything from slugs and snails, to bugs and butterflies and beetles and the wonders of ants and bees and termites, and things like that.
Anna - Why haven't there been more programmes like this?
Mike - There have been quite a few insects and other invertebrates featured in programmes. But I think we felt it was time for another in-depth look at them because the cameras are more sensitive, so you don't have to use so much light, and the improvements recently in the sorts of lenses we can use reveal a bit more of this fairly hidden world.
Anna - But the world is so big and insects are so small. How do you make sure you're in the right place at the right time?
Mike - Sometimes we haven't been in the right place at the right time, but that's really down to good research. For instance, we wanted to film the mass emergence of cicadas in the Eastern USA that actually only come out every 17 years. Luckily there are a number of people studying them and we hit upon a population that was going to emerge, or so the scientists told us, and indeed they did. We got a wonderful sequence.
Anna - Did you learn anything else that nobody knew about before?
Mike - Yes, I think there are several instances where our cameras revealed something that hadn't been noticed before. For instance, there are these weird clearings in the rainforest in the Amazon part of Peru that the locals call Devil's Gardens. They're a monoculture of one particular type of tree, and they give a home to tiny little black ants. There's a biologist called Megan Frederickson who's researching these things, and all of the saplings of other trees around this species were dying off. She knew it was something to do with the ants because the ants were visiting them but she didn't know how it happened. When we got our tiny lenses there, she saw for the first time that they were not only chewing into the outer bark but they were actually injecting formic acid into the wounds. And that's how these tiny ants were making these clearings bigger and bigger and bigger. Up to now, nobody knew how they did it.
Anna - What do you think people are going to be most surprised about by watching this?
Mike - I think they will be mostly surprised at the intricate behaviour that's happening all around them if you care to look. Why do hoverflies tend to stay in the same patch of sunlight, look around, and then suddenly dart off? What are they doing? They then come back to the same spot. Well we've done a sequence where we see that they're either chasing off rival males that come into their patch or they're showing off to females and then trying to mate with them as they fly off overhead. When people see that in detail, they'll be fascinated.
- Sequencing Genomes
with Dr Darren Grafham from the Sanger Centre in Hinxton, Cambridgeshire
Chris - What is the importance of sequencing big tracts of DNA?
Darren - Clearly it's important to understand the basics of who we are. It begins with the four letter code, the only four letters of the alphabet that really matter, A, C, T and G. The importance of these is that they're the building blocks for everything we do and everything that makes us. Once we have this, we can build on it to make advances in technology and medicine. Without knowing the genetic code, doing these things is really expensive and time consuming.
Chris - People told us that when we sequenced the human genome we'd have an idea of where all the human genes were. They said that research would be catapulted into the next dimension because we'd understand all about genetic disease. But about 15 years ago, someone published the entire sequence of the herpes simplex virus, that causes cold sores, and it's relative, the chicken pox virus. 90% of the population are still infected with those viruses and they're a major problem. We know the genetic code for them inside-out. So when are we going to see spin-offs from this that are actually going to allow us to cure people?
Darren - It all starts by making a road map, that is the DNA sequence. That gives us a road map but it doesn't tell us who lives in the houses along those streets. Until we know who lives in those houses, or in the case of the herpes simplex virus, what it does and how it interacts with things, we're still pretty lost as to how to stop it and prevent it. So it will take a number of years and some more advances. But once you have a street map, you have a starting point and you can make decisions about where to start looking and begin work.
Chris - Have there been any direct repercussions of the Human Genome Project?
Darren - It's difficult to answer. I think the most recent thing has been a number of cancer drugs that are just coming out and will go into clinical trials in the near future that may have taken another 10 or 15 years to get onto the market. By being able to know the DNA sequence and see the cancerous changes, you can use targeted drugs to actually start to produce medicines.
Chris - So you take the gene and have a look at what the gene makes. The this gives you an idea of what drugs might work against that particular structure.
Darren - That's right. It gives you some idea of what that protein does, including how it's made and how it functions.
- Insect evolution
with Dr Mike Majerus, Department of Genetics, University of Cambridge
Mike Majerus discusses the genetics of insects...
Kat - How similar are we to insects?
Mike - We're not very similar at all. If you look at our phenotype, which means the way we look, you can see we have a different number of eyes to some insects. We certainly have a different number of limbs. And yet when we go to the genetic level, we have an awful lot of genes the same. They're not exactly the same, but we can recognise that we have genes that do similar things. For example, we have very similar genes for respiration and DNA replication. In fact, for things like the genes for genetic replication, the similarities don't just stop at insects, but are found in pretty much all other forms of life.
Chris - If you look at something like a banana for example, I'm supposed to share about 60% of my genes with a banana. Would you go along with that?
Mike - Yes.
Kat - I'm getting images here of the film The Fly, where he wakes up and has turned into a fly. If you took a fly gene, would it work in humans?
Mike - That's the sort of question I'd really rather avoid, and I'll tell you why. There's this big feeling around the world that if the word genetics is mentioned, it's going to be something horrible. Most of the stories about genetically modified organisms are horror stories. Or there are mice with ears on their backs if we go back a decade or so. There's a phenomenal amount of genetics being done, but unfortunately you hardly ever hear about the good stories. There are two people I just want to mention. There's a guy called Dobzhansky, a Russian who went to America, and he said that nothing in biology makes sense except in the light of evolution. Then later, a couple of authors said nothing in evolution makes sense except in the light of genetics. If we're actually going to understand the world around us, we've got to understand genetics. It's the sort of thing that Darren's doing down at the Sanger Centre with his sequencing of vast amounts of DNA from different sorts of organisms that is beginning to give us a little bit of understanding of what's really going on.
Chris - Mike, you've also been doing some work on ladybirds. Apparently we've been invaded.
Mike - Oh yes. This is the killer Harlequin ladybird that arrived in the UK, and the first one was found on the 19th September 2004. It got into the press who made it into a very big story that it was going to wipe out all the British ladybirds. I'm responsible for that story. It's now increased its range so it's now all over the south east of England. We're getting huge numbers of records from the area that the Naked Scientists covers. We've had the first reports this autumn of houses being invaded by hundreds of these things. We've been working through the year and we've got funding for another year so that we can survey British ladybirds both where the Harlequin's arriving, and where it hasn't yet. We're doing genetics on this as well, as the Harlequin has lots of different colour forms. We're finding out the genetic control of those colours and we still want people to send us samples. If you can send us 40 or 50, we then get a frequency of the different samples and we can look at how evolution is affecting these colour patterns.
- Where is the best place to put a carbon monoxide detector?
Where is the best place to put a carbon monoxide detector?
He says the best place to put your carbon monoxide detector is either near your bed or your most dodgy gas appliance. This is because when carbon monoxide is in air, it won't rise up to the ceiling but will stay mixed in with everything else. Putting the detector near the most likely source or where you are most likely to suffer from carbon monoxide poisoning is the best plan of action. However, you do need to put smoke detectors near the ceiling because unlike carbon monoxide, smoke does rise.
- How is thunder and lightning made, and what causes it?
How is thunder and lightning made, and what causes it?
Storm clouds have lots of tiny particles in them, and these are called hydrometeors. These are tiny particles of ice crystals. In the same way as if you rub a balloon on your head and it can stick to the wall because of static electricity, when hydrometeors bounce together, they rub charge on and off each other. This makes charge get carried up and down within the cloud. This creates a difference in charge across the cloud, creating an electrical field. The result of this is that the Earth has a different electrical charge to the cloud. When the charge difference becomes big enough, eventually the insulation of the air breaks down and you get a lightning strike. A lightning bolt carries between a billion and 10 billion joules of energy, which is enough energy to make 100 000 pieces of toast! The lightning bolt is sufficient to heat the air around it to about 30 000 degrees centigrade - that's about six times the surface temperature of the sun. When you make something that hot, the gas molecules get so excited that you literally rip them to pieces. The electrons in the gas molecules jump to a very high energy level and then jump back again to a normal energy level. When they do that, they give out light. The light that they spray out is what you see as a flash of lightning. The sudden extreme heating of the air causes a compression wave, like clapping your hands together, around the lightning bolt, and that's what slowly propagates to you as a roll of thunder. As light travels much faster than sound waves, that's why you see the lightning first and then you hear the thunder.
- Why does putting crackers in a box keep them fresh?
Why does putting crackers in a box keep them fresh?
When you put crackers into a tin, the amount of air, and thus water in the air, is limited. Thus, even though they'll soak up some water, they don't have access to a whole room's worth of water, and so the amount of water available to make them soft and stale is minimal.
- If human and worm DNA are so similar, why are we so different?
If human and worm DNA are so similar, why are we so different?
There are certain major genes, sometimes called Hox genes and sometimes called developmental genes, that switch on a whole suite of other genes. They are simply like switches in early developmental processes. To give an example that's a little bit closer to home, look for the nearest man and see how different you are from that person. Now although not everything that's different is down to one gene, the fact that you are female and he is male is down to a single gene called SRY. Very early in development, if SRY is present it makes testes, and if it's not, ovaries are made. So you've got just one single gene that switches over from one type to another, and then everything else follows from that, including the hormones produced by testes and ovaries. In worms, they've got a different set of these Hox genes, which start the whole process off. They're switching on a completely different set of genes in a different order, and so the developmental process is utterly different.
- What is Fragile X syndrome?
What is Fragile X syndrome?
Chris - This is one of these very interesting classes of diseases where pieces of DNA can change their lengths in an unpredictable way. There's a whole family of this type of diseases and they often affect the brain. This is probably because the brain expresses about 80% of the genes in our body. Therefore, if you have a problem with a particular gene, it will manifest itself in some way in the brain.
With fragile X, we know that one part of the X-chromosome becomes longer than it should do, and it causes genes adjacent to the bits that get too big to behave a bit abnormally.
Whether or not we are in the position to make any differences to those people very soon, I think the answer's probably no.
Mike - Fragile X is called a triplet repeat disease. This is because there are a specific three nucleotides - that's the A, T, G and Cs that Darren was talking about earlier - that repeat themselves a number of times. Everyone has this particular section repeated, but normally it's a limited number of repeats. You may have heard of the idea of the selfish gene. Well there's also selfish DNA. This is bits of DNA that try to replicate themselves and keep going not through the generations but within the cell generations in an organism. And so they make more copies of themselves, partly by unequal crossing over, and it's once you've passed a particular threshold of the number of triplet repeats that you get problems.
The same is true of Huntington's chorea, and there are about four of these diseases.
- How many different types of DNA can you get?
How many different types of DNA can you get?
There are two answers to this question. One is that there is only a single type of DNA, as it's all made up of the same basic codes. However, there are certain sub-types of DNA. These include cDNA, which stands for coding DNA, and single stranded DNA, which looks like a ladder cut in half.